TCGA-Assembler: open-source software for retrieving and processing TCGA data von Zhu, Yitan, Qiu, Peng, Ji, Yuan

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TCGA-assembler 2: software pipeline for retrieval and processing of TCGA/CPTAC data von Wei, Lin, Jin, Zhilin, Yang, Shengjie, Xu, Yanxun, Zhu, Yitan, Ji, Yuan

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Prediction of chronic kidney disease progression using recurrent neural network and electronic health records von Zhu, Yitan, Bi, Dehua, Saunders, Milda, Ji, Yuan

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Converting tabular data into images for deep learning with convolutional neural networks von Zhu, Yitan, Brettin, Thomas, Xia, Fangfang, Partin, Alexander, Shukla, Maulik, Yoo, Hyunseung, Evrard, Yvonne A., Doroshow, James H., Stevens, Rick L.

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MR Imaging Radiomics Signatures for Predicting the Risk of Breast Cancer Recurrence as Given by Research Versions of MammaPrint, Oncotype DX, and PAM50 Gene Assays von Li, Hui, Zhu, Yitan, Burnside, Elizabeth S, Drukker, Karen, Hoadley, Katherine A, Fan, Cheng, Conzen, Suzanne D, Whitman, Gary J, Sutton, Elizabeth J, Net, Jose M, Ganott, Marie, Huang, Erich, Morris, Elizabeth A, Perou, Charles M, Ji, Yuan, Giger, Maryellen L

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A Chaperome Subnetwork Safeguards Proteostasis in Aging and Neurodegenerative Disease von Brehme, Marc, Voisine, Cindy, Rolland, Thomas, Wachi, Shinichiro, Soper, James H., Zhu, Yitan, Orton, Kai, Villella, Adriana, Garza, Dan, Vidal, Marc, Ge, Hui, Morimoto, Richard I.

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Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma von Zhu, Yitan, Li, Hui, Guo, Wentian, Drukker, Karen, Lan, Li, Giger, Maryellen L., Ji, Yuan

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Deep learning methods for drug response prediction in cancer: Predominant and emerging trends von Partin, Alexander, Brettin, Thomas S, Zhu, Yitan, Narykov, Oleksandr, Clyde, Austin, Overbeek, Jamie, Stevens, Rick L

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Publisher Correction: Converting tabular data into images for deep learning with convolutional neural networks von Zhu, Yitan, Brettin, Thomas, Xia, Fangfang, Partin, Alexander, Shukla, Maulik, Yoo, Hyunseung, Evrard, Yvonne A., Doroshow, James H., Stevens, Rick L.

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Learning curves for drug response prediction in cancer cell lines von Partin, Alexander, Brettin, Thomas, Evrard, Yvonne A, Zhu, Yitan, Yoo, Hyunseung, Xia, Fangfang, Jiang, Songhao, Clyde, Austin, Shukla, Maulik, Fonstein, Michael, Doroshow, James H, Stevens, Rick L

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Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA data set von Li, Hui, Zhu, Yitan, Burnside, Elizabeth S, Huang, Erich, Drukker, Karen, Hoadley, Katherine A, Fan, Cheng, Conzen, Suzanne D, Zuley, Margarita, Net, Jose M, Sutton, Elizabeth, Whitman, Gary J, Morris, Elizabeth, Perou, Charles M, Ji, Yuan, Giger, Maryellen L

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Radiogenomics of breast cancer using dynamic contrast enhanced MRI and gene expression profiling von Yeh, Albert C, Li, Hui, Zhu, Yitan, Zhang, Jing, Khramtsova, Galina, Drukker, Karen, Edwards, Alexandra, McGregor, Stephanie, Yoshimatsu, Toshio, Zheng, Yonglan, Niu, Qun, Abe, Hiroyuki, Mueller, Jeffrey, Conzen, Suzanne, Ji, Yuan, Giger, Maryellen L, Olopade, Olufunmilayo I

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Prediction of clinical phenotypes in invasive breast carcinomas from the integration of radiomics and genomics data von Guo, Wentian, Li, Hui, Zhu, Yitan, Lan, Li, Yang, Shengjie, Drukker, Karen, Morris, Elizabeth, Burnside, Elizabeth, Whitman, Gary, Giger, Maryellen L, Ji, Yuan, TCGA Breast Phenotype Research Group

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Nuclear envelope dystrophies show a transcriptional fingerprint suggesting disruption of Rb–MyoD pathways in muscle regeneration von Bakay, Marina, Wang, Zuyi, Melcon, Gisela, Schiltz, Louis, Xuan, Jianhua, Zhao, Po, Sartorelli, Vittorio, Seo, Jinwook, Pegoraro, Elena, Angelini, Corrado, Shneiderman, Ben, Escolar, Diana, Chen, Yi-Wen, Winokur, Sara T., Pachman, Lauren M., Fan, Chenguang, Mandler, Raul, Nevo, Yoram, Gordon, Erynn, Zhu, Yitan, Dong, Yibin, Wang, Yue, Hoffman, Eric P.

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Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data von Zhu, Yitan, Xu, Yanxun, Helseth, Jr, Donald L, Gulukota, Kamalakar, Yang, Shengjie, Pesce, Lorenzo L, Mitra, Riten, Müller, Peter, Sengupta, Subhajit, Guo, Wentian, Silverstein, Jonathan C, Foster, Ian, Parsad, Nigel, White, Kevin P, Ji, Yuan

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TU-A-207B-00: Imaging Genomics Associations and Biological Correlates of Radiomics von Zhu, Yitan

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Initialization enhancer for non-negative matrix factorization von Zheng, Zhonglong, Yang, Jie, Zhu, Yitan

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Data augmentation and multimodal learning for predicting drug response in patient-derived xenografts from gene expressions and histology images von Partin, Alexander, Brettin, Thomas, Zhu, Yitan, Dolezal, James M, Kochanny, Sara, Pearson, Alexander T, Shukla, Maulik, Evrard, Yvonne A, Doroshow, James H, Stevens, Rick L

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Heterogeneous Reciprocal Graphical Models von Ni, Yang, Müller, Peter, Zhu, Yitan, Ji, Yuan

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Characterizing Cancer-Specific Networks by Integrating TCGA Data von Xu, Yanxun, Zhu, Yitan, Müller, Peter, Mitra, Riten, Ji, Yuan

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